3cbb47a8eef0a0aa7f0ea8041396ce4f microorganisms_a2021v9n8p1629.pdf 379e7061e7e9adfef60140f6e131225864f82580 microorganisms_a2021v9n8p1629.pdf 8b5fb966513d4580dc15a33d41d38633ad8b2d32faf35d1b57eebdcb13c5cf91 microorganisms_a2021v9n8p1629.pdf Title: Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain Subject: The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting. Keywords: whole-genome sequencing; SNP; Mycobacterium bovis; bovine tuberculosis; Catalonia; northeastern Spain Author: Claudia Perea, Giovanna Ciaravino, Tod Stuber, Tyler C. Thacker, Suelee Robbe-Austerman, Alberto Allepuz and Bernat Pérez de Val Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Thu Aug 19 05:09:34 2021 CEST ModDate: Thu Aug 19 05:12:28 2021 CEST Tagged: no UserProperties: no Suspects: no Form: none JavaScript: no Pages: 24 Encrypted: no Page size: 595.276 x 841.89 pts (A4) Page rot: 0 File size: 1591644 bytes Optimized: no PDF version: 1.7 name type encoding emb sub uni object ID ------------------------------------ ----------------- ---------------- --- --- --- --------- UOHDZX+VnURWPalladioL Type 1 Custom yes yes no 10 0 VCEOPQ+URWPalladioL-Ital Type 1 Custom yes yes no 15 0 QLXOZX+URWPalladioL-Bold Type 1 Custom yes yes no 20 0 NMSLAD+URWPalladioL-BoldItal Type 1 Custom yes yes no 24 0 APDWXI+URWPalladioL-Roma Type 1 Custom yes yes no 28 0 TKGLZS+CMSY10 Type 1 Builtin yes yes no 32 0 BTFGED+VnURWPalladioL-Bold Type 1 Custom yes yes no 36 0 SIXRFS+TimesNewRomanPS-BoldItalicMT Type 1C WinAnsi yes yes no 44 0 MCBCCI+SourceSansRoman-Regular Type 1C Custom yes yes no 66 0 MCBCCM+SourceSansRoman.613wght Type 1C Custom yes yes no 70 0 MCBCCO+SourceSansRoman-Bold Type 1C Custom yes yes no 74 0 OVNEXW+EURM10 Type 1 Builtin yes yes no 97 0 UFCNWC+Arimo-Regular TrueType WinAnsi yes yes yes 116 0 OROVRK+Arimo-Italic TrueType WinAnsi yes yes yes 120 0 CVHQTK+Arimo-Bold TrueType WinAnsi yes yes yes 124 0 ALBBUL+VnURWPalladioL-Italic Type 1 Custom yes yes no 183 0 BOLMEN+SFRM0900 Type 1 Custom yes yes no 194 0 Jhove (Rel. 1.22.1, 2019-04-17) Date: 2022-03-05 02:45:05 CET RepresentationInformation: microorganisms_a2021v9n8p1629.pdf ReportingModule: PDF-hul, Rel. 1.12.1 (2019-04-17) LastModified: 2022-01-21 11:42:01 CET Size: 1591644 Format: PDF Version: 1.7 Status: Well-Formed and valid SignatureMatches: PDF-hul MIMEtype: application/pdf PDFMetadata: Objects: 512 FreeObjects: 1 IncrementalUpdates: 0 DocumentCatalog: PageLayout: SinglePage PageMode: UseNone Outlines: Item: Title: Introduction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7b69c6ba Item: Title: Materials and Methods Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@46daef40 Children: Item: Title: Sampling Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@12f41634 Item: Title: MTBC Isolation and Identification Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@13c27452 Item: Title: DNA Extraction Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@262b2c86 Item: Title: Whole-Genome Sequencing and SNP Analysis Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@371a67ec Item: Title: Characterization of Antibiotic-Resistant Mutations and SNP on Virulence Genes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@5ed828d Item: Title: In Silico DVR-Spoligotyping Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@50d0686 Item: Title: Epidemiological Associations Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@7a3d45bd Item: Title: Results Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1e7c7811 Children: Item: Title: Spoligotyping Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77ec78b9 Item: Title: WGS-Based Phylogenetic Structure of MTBC Isolates from Catalonia Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@1a3869f4 Item: Title: Epidemiological Investigations and Putative Transmission Clusters Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@a38d7a3 Item: Title: Cross-Sectional Data Analysis in a World Context Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@77f99a05 Item: Title: Virulence and Antimicrobial Resistance Traits Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@63440df3 Item: Title: Discussion Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@3aeaafa6 Children: Item: Title: Isolates’ Demographic Attributes Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@76a3e297 Item: Title: Genetic Diversity Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4d3167f4 Item: Title: Transmission Clusters Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@ed9d034 Item: Title: Catalonia M. bovis in a World Context Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@6121c9d6 Item: Title: Virulence and Antibiotic Resistance Factors Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@87f383f Item: Title: Conclusions Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@4eb7f003 Item: Title: References Destination: edu.harvard.hul.ois.jhove.module.pdf.PdfSimpleObject@eafc191 Info: Title: Whole-Genome SNP Analysis Identifies Putative Mycobacterium bovis Transmission Clusters in Livestock and Wildlife in Catalonia, Spain Author: Claudia Perea, Giovanna Ciaravino, Tod Stuber, Tyler C. Thacker, Suelee Robbe-Austerman, Alberto Allepuz and Bernat Pérez de Val Subject: The high-resolution WGS analyses of MTBC strains have provided useful insight for determining sources of infection for animal tuberculosis. In Spain, tuberculosis in livestock is caused by Mycobacterium bovis and Mycobacterium caprae, where wildlife reservoirs play an important role. We analyzed a set of 125 M. bovis isolates obtained from livestock and wildlife from Catalonia to investigate strain diversity and identify possible sources and/or causes of infection. Whole-genome SNP profiles were used for phylogenetic reconstruction and pairwise SNP distance analysis. Additionally, SNPs were investigated to identify virulence and antimicrobial resistance factors to investigate clade-specific associations. Putative transmission clusters (12 SNPs) were identified, and associated epidemiological metadata were used to determine possible explanatory factors for transmission. M. bovis distribution was heterogeneous, with 7 major clades and 21 putative transmission clusters. In order of importance, the explanatory factors associated were proximity and neighborhood, residual infection, livestock-wildlife interaction, shared pasture, and movement. Genes related to lipid transport and metabolism showed the highest number of SNPs. All isolates were pyrazinamide resistant, and five were additionally resistant to isoniazid, but no clade-specific associations could be determined. Our findings highlight the importance of high-resolution molecular surveillance to monitor bovine tuberculosis dynamics in a low-prevalence setting. Keywords: whole-genome sequencing; SNP; Mycobacterium bovis; bovine tuberculosis; Catalonia; northeastern Spain Creator: LaTeX with hyperref Producer: pdfTeX-1.40.21 CreationDate: Thu Aug 19 05:09:34 CEST 2021 ModDate: Thu Aug 19 05:12:28 CEST 2021 ID: 0x84814069b67fda96eff36a8f510c1e78, 0x84814069b67fda96eff36a8f510c1e78 Filters: FilterPipeline: FlateDecode Fonts: Type1: Font: BaseFont: TKGLZS+CMSY10 FontSubset: true FirstChar: 0 LastChar: 36 FontDescriptor: FontName: TKGLZS+CMSY10 Flags: Symbolic FontBBox: -29, -960, 1116, 775 FontFile: true Font: BaseFont: OVNEXW+EURM10 FontSubset: true FirstChar: 22 LastChar: 22 FontDescriptor: FontName: OVNEXW+EURM10 Flags: Symbolic FontBBox: -32, -243, 1060, 720 FontFile: true Font: BaseFont: BOLMEN+SFRM0900 FontSubset: true FirstChar: 180 LastChar: 180 FontDescriptor: FontName: BOLMEN+SFRM0900 Flags: Symbolic FontBBox: -196, -322, 1502, 937 FontFile: true EncodingDictionary: Differences: true Font: BaseFont: QLXOZX+URWPalladioL-Bold FontSubset: 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CRC32 Checksum: 3cbb47a8eef0a0aa7f0ea8041396ce4f Type: MD5 Checksum: 379e7061e7e9adfef60140f6e131225864f82580 Type: SHA-1